Starting phenix.real_space_refine on Mon Jun 16 05:52:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.map" model { file = "/net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7boz_30137/06_2025/7boz_30137.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.319 sd= 0.994 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 11640 2.51 5 N 3282 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18516 Number of models: 1 Model: "" Number of chains: 18 Chain: "a" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "b" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "c" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "d" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "e" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "g" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "h" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "i" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "j" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "k" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "l" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "m" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "n" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "o" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "p" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "q" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "r" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Time building chain proxies: 11.77, per 1000 atoms: 0.64 Number of scatterers: 18516 At special positions: 0 Unit cell: (207.01, 226.06, 77.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 3576 8.00 N 3282 7.00 C 11640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 36 sheets defined 21.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'a' and resid 28 through 30 No H-bonds generated for 'chain 'a' and resid 28 through 30' Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 95 through 121 removed outlier: 3.510A pdb=" N THR a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR a 118 " --> pdb=" O ARG a 114 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE a 121 " --> pdb=" O THR a 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 95 through 113 removed outlier: 3.627A pdb=" N LEU b 99 " --> pdb=" O ARG b 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 106 " --> pdb=" O ALA b 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET b 107 " --> pdb=" O GLN b 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 30 No H-bonds generated for 'chain 'c' and resid 28 through 30' Processing helix chain 'c' and resid 95 through 116 removed outlier: 3.656A pdb=" N ASN c 100 " --> pdb=" O ALA c 96 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR c 106 " --> pdb=" O ALA c 102 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP c 115 " --> pdb=" O GLU c 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU c 116 " --> pdb=" O GLU c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 30 No H-bonds generated for 'chain 'd' and resid 28 through 30' Processing helix chain 'd' and resid 45 through 49 Processing helix chain 'd' and resid 95 through 121 removed outlier: 3.750A pdb=" N THR d 118 " --> pdb=" O ARG d 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 113 removed outlier: 3.696A pdb=" N MET e 107 " --> pdb=" O GLN e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 30 No H-bonds generated for 'chain 'f' and resid 28 through 30' Processing helix chain 'f' and resid 95 through 116 removed outlier: 3.676A pdb=" N ASN f 100 " --> pdb=" O ALA f 96 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN f 103 " --> pdb=" O LEU f 99 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR f 106 " --> pdb=" O ALA f 102 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA f 110 " --> pdb=" O THR f 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP f 115 " --> pdb=" O GLU f 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU f 116 " --> pdb=" O GLU f 112 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 30 No H-bonds generated for 'chain 'g' and resid 28 through 30' Processing helix chain 'g' and resid 45 through 49 Processing helix chain 'g' and resid 95 through 121 removed outlier: 3.813A pdb=" N THR g 118 " --> pdb=" O ARG g 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE g 121 " --> pdb=" O THR g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 113 removed outlier: 3.582A pdb=" N MET h 107 " --> pdb=" O GLN h 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA h 110 " --> pdb=" O THR h 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 30 No H-bonds generated for 'chain 'i' and resid 28 through 30' Processing helix chain 'i' and resid 95 through 116 removed outlier: 3.694A pdb=" N ASN i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN i 103 " --> pdb=" O LEU i 99 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR i 106 " --> pdb=" O ALA i 102 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA i 110 " --> pdb=" O THR i 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP i 115 " --> pdb=" O GLU i 111 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU i 116 " --> pdb=" O GLU i 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 30 No H-bonds generated for 'chain 'j' and resid 28 through 30' Processing helix chain 'j' and resid 45 through 49 removed outlier: 3.537A pdb=" N ASP j 49 " --> pdb=" O THR j 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 45 through 49' Processing helix chain 'j' and resid 95 through 121 removed outlier: 3.924A pdb=" N THR j 118 " --> pdb=" O ARG j 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE j 121 " --> pdb=" O THR j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 113 removed outlier: 3.628A pdb=" N LEU k 99 " --> pdb=" O ARG k 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET k 107 " --> pdb=" O GLN k 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 114 through 116 No H-bonds generated for 'chain 'k' and resid 114 through 116' Processing helix chain 'l' and resid 28 through 30 No H-bonds generated for 'chain 'l' and resid 28 through 30' Processing helix chain 'l' and resid 95 through 116 removed outlier: 3.724A pdb=" N ASN l 100 " --> pdb=" O ALA l 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN l 103 " --> pdb=" O LEU l 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR l 106 " --> pdb=" O ALA l 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP l 115 " --> pdb=" O GLU l 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU l 116 " --> pdb=" O GLU l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 30 No H-bonds generated for 'chain 'm' and resid 28 through 30' Processing helix chain 'm' and resid 45 through 49 removed outlier: 3.503A pdb=" N ASP m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 45 through 49' Processing helix chain 'm' and resid 95 through 121 removed outlier: 3.537A pdb=" N ALA m 110 " --> pdb=" O THR m 106 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE m 121 " --> pdb=" O THR m 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 95 through 113 removed outlier: 3.730A pdb=" N LEU n 99 " --> pdb=" O ARG n 95 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR n 106 " --> pdb=" O ALA n 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET n 107 " --> pdb=" O GLN n 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 116 No H-bonds generated for 'chain 'n' and resid 114 through 116' Processing helix chain 'o' and resid 28 through 30 No H-bonds generated for 'chain 'o' and resid 28 through 30' Processing helix chain 'o' and resid 95 through 118 removed outlier: 3.681A pdb=" N ASN o 100 " --> pdb=" O ALA o 96 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR o 106 " --> pdb=" O ALA o 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS o 108 " --> pdb=" O ILE o 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL o 109 " --> pdb=" O GLN o 105 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA o 110 " --> pdb=" O THR o 106 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP o 115 " --> pdb=" O GLU o 111 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU o 116 " --> pdb=" O GLU o 112 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR o 117 " --> pdb=" O ALA o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 30 No H-bonds generated for 'chain 'p' and resid 28 through 30' Processing helix chain 'p' and resid 45 through 49 Processing helix chain 'p' and resid 95 through 121 removed outlier: 3.559A pdb=" N ALA p 110 " --> pdb=" O THR p 106 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR p 118 " --> pdb=" O ARG p 114 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE p 121 " --> pdb=" O THR p 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 113 removed outlier: 3.727A pdb=" N LEU q 99 " --> pdb=" O ARG q 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR q 106 " --> pdb=" O ALA q 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET q 107 " --> pdb=" O GLN q 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 30 No H-bonds generated for 'chain 'r' and resid 28 through 30' Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 95 through 118 removed outlier: 3.650A pdb=" N ASN r 100 " --> pdb=" O ALA r 96 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN r 103 " --> pdb=" O LEU r 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS r 108 " --> pdb=" O ILE r 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL r 109 " --> pdb=" O GLN r 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA r 110 " --> pdb=" O THR r 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP r 115 " --> pdb=" O GLU r 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU r 116 " --> pdb=" O GLU r 112 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR r 117 " --> pdb=" O ALA r 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'a' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'a' and resid 122 through 123 removed outlier: 3.944A pdb=" N GLY a 122 " --> pdb=" O ALA a 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 9 through 10 removed outlier: 3.741A pdb=" N LEU b 9 " --> pdb=" O LEU b 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU b 75 " --> pdb=" O LEU b 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'd' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'd' and resid 19 through 21 Processing sheet with id=AA9, first strand: chain 'd' and resid 122 through 123 removed outlier: 3.891A pdb=" N GLY d 122 " --> pdb=" O ALA d 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 9 through 10 removed outlier: 3.690A pdb=" N LEU e 9 " --> pdb=" O LEU e 75 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 75 " --> pdb=" O LEU e 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'f' and resid 32 through 33 Processing sheet with id=AB4, first strand: chain 'g' and resid 8 through 12 Processing sheet with id=AB5, first strand: chain 'g' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'g' and resid 122 through 123 removed outlier: 3.824A pdb=" N GLY g 122 " --> pdb=" O ALA g 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 9 through 10 removed outlier: 3.697A pdb=" N LEU h 9 " --> pdb=" O LEU h 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU h 75 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 20 through 21 Processing sheet with id=AB9, first strand: chain 'i' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'j' and resid 8 through 12 Processing sheet with id=AC2, first strand: chain 'j' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'j' and resid 122 through 123 removed outlier: 3.878A pdb=" N GLY j 122 " --> pdb=" O ALA j 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 9 through 10 removed outlier: 3.762A pdb=" N LEU k 9 " --> pdb=" O LEU k 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU k 75 " --> pdb=" O LEU k 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'k' and resid 19 through 21 Processing sheet with id=AC6, first strand: chain 'l' and resid 32 through 33 Processing sheet with id=AC7, first strand: chain 'm' and resid 8 through 10 Processing sheet with id=AC8, first strand: chain 'm' and resid 19 through 21 Processing sheet with id=AC9, first strand: chain 'm' and resid 122 through 123 removed outlier: 3.970A pdb=" N GLY m 122 " --> pdb=" O ALA m 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 9 through 10 removed outlier: 3.698A pdb=" N LEU n 9 " --> pdb=" O LEU n 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU n 75 " --> pdb=" O LEU n 9 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'n' and resid 19 through 21 Processing sheet with id=AD3, first strand: chain 'o' and resid 32 through 33 Processing sheet with id=AD4, first strand: chain 'p' and resid 8 through 10 Processing sheet with id=AD5, first strand: chain 'p' and resid 19 through 21 Processing sheet with id=AD6, first strand: chain 'p' and resid 122 through 123 removed outlier: 3.988A pdb=" N GLY p 122 " --> pdb=" O ALA p 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'q' and resid 9 through 10 removed outlier: 3.814A pdb=" N LEU q 9 " --> pdb=" O LEU q 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU q 75 " --> pdb=" O LEU q 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'q' and resid 19 through 21 Processing sheet with id=AD9, first strand: chain 'r' and resid 32 through 33 434 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3916 1.33 - 1.45: 4248 1.45 - 1.57: 10537 1.57 - 1.69: 19 1.69 - 1.81: 36 Bond restraints: 18756 Sorted by residual: bond pdb=" N ASN h 138 " pdb=" CA ASN h 138 " ideal model delta sigma weight residual 1.458 1.524 -0.066 1.90e-02 2.77e+03 1.21e+01 bond pdb=" N ASN e 138 " pdb=" CA ASN e 138 " ideal model delta sigma weight residual 1.458 1.523 -0.065 1.90e-02 2.77e+03 1.15e+01 bond pdb=" CB ILE p 93 " pdb=" CG2 ILE p 93 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" N ASN b 138 " pdb=" CA ASN b 138 " ideal model delta sigma weight residual 1.458 1.522 -0.064 1.90e-02 2.77e+03 1.13e+01 bond pdb=" CA ASN q 138 " pdb=" CB ASN q 138 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 18751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 24801 4.95 - 9.89: 596 9.89 - 14.84: 98 14.84 - 19.78: 5 19.78 - 24.73: 6 Bond angle restraints: 25506 Sorted by residual: angle pdb=" C ILE k 136 " pdb=" N VAL k 137 " pdb=" CA VAL k 137 " ideal model delta sigma weight residual 121.97 135.78 -13.81 1.80e+00 3.09e-01 5.89e+01 angle pdb=" C ILE h 136 " pdb=" N VAL h 137 " pdb=" CA VAL h 137 " ideal model delta sigma weight residual 121.97 135.78 -13.81 1.80e+00 3.09e-01 5.88e+01 angle pdb=" C ILE n 136 " pdb=" N VAL n 137 " pdb=" CA VAL n 137 " ideal model delta sigma weight residual 121.97 135.67 -13.70 1.80e+00 3.09e-01 5.79e+01 angle pdb=" C ILE e 136 " pdb=" N VAL e 137 " pdb=" CA VAL e 137 " ideal model delta sigma weight residual 121.97 135.57 -13.60 1.80e+00 3.09e-01 5.70e+01 angle pdb=" C ILE q 136 " pdb=" N VAL q 137 " pdb=" CA VAL q 137 " ideal model delta sigma weight residual 121.97 135.48 -13.51 1.80e+00 3.09e-01 5.63e+01 ... (remaining 25501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 9988 14.43 - 28.85: 842 28.85 - 43.28: 310 43.28 - 57.71: 67 57.71 - 72.14: 13 Dihedral angle restraints: 11220 sinusoidal: 4416 harmonic: 6804 Sorted by residual: dihedral pdb=" CA PRO c 23 " pdb=" C PRO c 23 " pdb=" N PHE c 24 " pdb=" CA PHE c 24 " ideal model delta harmonic sigma weight residual 180.00 116.69 63.31 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA PRO i 23 " pdb=" C PRO i 23 " pdb=" N PHE i 24 " pdb=" CA PHE i 24 " ideal model delta harmonic sigma weight residual 180.00 116.85 63.15 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA PRO r 23 " pdb=" C PRO r 23 " pdb=" N PHE r 24 " pdb=" CA PHE r 24 " ideal model delta harmonic sigma weight residual 180.00 116.90 63.10 0 5.00e+00 4.00e-02 1.59e+02 ... (remaining 11217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2626 0.094 - 0.189: 437 0.189 - 0.283: 78 0.283 - 0.378: 5 0.378 - 0.472: 10 Chirality restraints: 3156 Sorted by residual: chirality pdb=" CG LEU f 13 " pdb=" CB LEU f 13 " pdb=" CD1 LEU f 13 " pdb=" CD2 LEU f 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB VAL n 137 " pdb=" CA VAL n 137 " pdb=" CG1 VAL n 137 " pdb=" CG2 VAL n 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CB VAL q 137 " pdb=" CA VAL q 137 " pdb=" CG1 VAL q 137 " pdb=" CG2 VAL q 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 3153 not shown) Planarity restraints: 3228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE r 22 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ILE r 22 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE r 22 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO r 23 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE l 22 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE l 22 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE l 22 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO l 23 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE o 22 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C ILE o 22 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE o 22 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO o 23 " -0.021 2.00e-02 2.50e+03 ... (remaining 3225 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 774 2.69 - 3.24: 18071 3.24 - 3.80: 28921 3.80 - 4.35: 34911 4.35 - 4.90: 56317 Nonbonded interactions: 138994 Sorted by model distance: nonbonded pdb=" OH TYR p 26 " pdb=" O ARG p 55 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR a 26 " pdb=" O ARG a 55 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR m 26 " pdb=" O ARG m 55 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR k 11 " pdb=" O ASN k 21 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR n 11 " pdb=" O ASN n 21 " model vdw 2.184 3.040 ... (remaining 138989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'a' and resid 6 through 124) selection = (chain 'b' and resid 6 through 124) selection = chain 'c' selection = (chain 'd' and resid 6 through 124) selection = (chain 'e' and resid 6 through 124) selection = chain 'f' selection = (chain 'g' and resid 6 through 124) selection = (chain 'h' and resid 6 through 124) selection = chain 'i' selection = (chain 'j' and resid 6 through 124) selection = (chain 'k' and resid 6 through 124) selection = chain 'l' selection = (chain 'm' and resid 6 through 124) selection = (chain 'n' and resid 6 through 124) selection = chain 'o' selection = (chain 'p' and resid 6 through 124) selection = (chain 'q' and resid 6 through 124) selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.390 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.111 18756 Z= 0.466 Angle : 1.846 24.731 25506 Z= 0.975 Chirality : 0.077 0.472 3156 Planarity : 0.010 0.089 3228 Dihedral : 13.233 72.137 6804 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 1.54 % Allowed : 13.14 % Favored : 85.32 % Rotamer: Outliers : 1.32 % Allowed : 6.42 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 2.12 % Twisted Proline : 33.33 % Twisted General : 5.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.12), residues: 2268 helix: -3.85 (0.12), residues: 474 sheet: -3.46 (0.22), residues: 324 loop : -3.75 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP q 64 HIS 0.022 0.007 HIS a 108 PHE 0.032 0.004 PHE f 20 TYR 0.045 0.005 TYR q 11 ARG 0.017 0.002 ARG p 84 Details of bonding type rmsd hydrogen bonds : bond 0.31690 ( 434) hydrogen bonds : angle 9.48339 ( 1245) covalent geometry : bond 0.01044 (18756) covalent geometry : angle 1.84588 (25506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 883 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 60 LEU cc_start: 0.8289 (mt) cc_final: 0.8029 (mp) REVERT: b 8 VAL cc_start: 0.9245 (t) cc_final: 0.8846 (p) REVERT: b 13 LEU cc_start: 0.7247 (pp) cc_final: 0.6932 (pp) REVERT: c 40 ASP cc_start: 0.7269 (m-30) cc_final: 0.6911 (m-30) REVERT: c 80 SER cc_start: 0.9001 (p) cc_final: 0.8415 (t) REVERT: d 141 ASN cc_start: 0.7465 (t0) cc_final: 0.6988 (t0) REVERT: e 9 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8395 (pp) REVERT: e 45 THR cc_start: 0.8293 (m) cc_final: 0.8014 (m) REVERT: e 115 ASP cc_start: 0.7374 (m-30) cc_final: 0.7172 (m-30) REVERT: f 59 SER cc_start: 0.7518 (m) cc_final: 0.7221 (p) REVERT: f 70 TYR cc_start: 0.6452 (m-10) cc_final: 0.6181 (m-10) REVERT: g 115 ASP cc_start: 0.8211 (t70) cc_final: 0.7531 (t70) REVERT: i 59 SER cc_start: 0.7945 (m) cc_final: 0.7304 (p) REVERT: i 80 SER cc_start: 0.7882 (p) cc_final: 0.7246 (t) REVERT: j 115 ASP cc_start: 0.7724 (t70) cc_final: 0.7137 (t70) REVERT: k 86 VAL cc_start: 0.8865 (t) cc_final: 0.8411 (t) REVERT: k 136 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.6920 (pt) REVERT: l 6 LYS cc_start: 0.7918 (pmtt) cc_final: 0.7602 (ptpp) REVERT: l 80 SER cc_start: 0.7667 (p) cc_final: 0.6509 (t) REVERT: l 93 ILE cc_start: 0.7434 (pp) cc_final: 0.7209 (pt) REVERT: l 115 ASP cc_start: 0.7278 (t70) cc_final: 0.6561 (t0) REVERT: l 121 ILE cc_start: 0.7480 (mm) cc_final: 0.7224 (mm) REVERT: m 58 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8740 (pp) REVERT: m 111 GLU cc_start: 0.7495 (tp30) cc_final: 0.6992 (tp30) REVERT: n 8 VAL cc_start: 0.8829 (t) cc_final: 0.8489 (m) REVERT: n 57 THR cc_start: 0.8224 (p) cc_final: 0.7777 (t) REVERT: n 107 MET cc_start: 0.7889 (mtp) cc_final: 0.7491 (mtm) REVERT: n 136 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5135 (pp) REVERT: o 6 LYS cc_start: 0.7116 (pmtt) cc_final: 0.6842 (ptpp) REVERT: o 8 VAL cc_start: 0.7284 (t) cc_final: 0.7038 (p) REVERT: o 49 ASP cc_start: 0.7810 (m-30) cc_final: 0.7515 (m-30) REVERT: p 13 LEU cc_start: 0.7631 (tt) cc_final: 0.7019 (tp) REVERT: p 58 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.7856 (pp) REVERT: p 118 THR cc_start: 0.8202 (m) cc_final: 0.7929 (m) REVERT: q 136 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.6017 (pt) REVERT: r 6 LYS cc_start: 0.7703 (pmtt) cc_final: 0.7337 (pptt) REVERT: r 8 VAL cc_start: 0.7136 (t) cc_final: 0.6905 (p) REVERT: r 40 ASP cc_start: 0.8041 (m-30) cc_final: 0.7237 (p0) REVERT: r 70 TYR cc_start: 0.5140 (m-10) cc_final: 0.4545 (m-10) REVERT: r 115 ASP cc_start: 0.5617 (t70) cc_final: 0.4860 (t0) outliers start: 27 outliers final: 0 residues processed: 902 average time/residue: 0.3566 time to fit residues: 457.4882 Evaluate side-chains 447 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 441 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain m residue 58 ILE Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain p residue 58 ILE Chi-restraints excluded: chain q residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 113 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 HIS d 103 GLN f 103 GLN ** h 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 GLN k 108 HIS ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 108 HIS o 108 HIS p 12 GLN r 17 ASN r 108 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088047 restraints weight = 60136.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089328 restraints weight = 36999.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090204 restraints weight = 26893.390| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18756 Z= 0.186 Angle : 0.983 12.875 25506 Z= 0.506 Chirality : 0.050 0.254 3156 Planarity : 0.006 0.084 3228 Dihedral : 9.059 60.073 2616 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.71 % Favored : 88.71 % Rotamer: Outliers : 4.41 % Allowed : 18.87 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 1.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.15), residues: 2268 helix: -1.96 (0.20), residues: 456 sheet: -2.54 (0.27), residues: 258 loop : -2.95 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP o 64 HIS 0.009 0.003 HIS m 108 PHE 0.022 0.002 PHE i 24 TYR 0.024 0.002 TYR f 97 ARG 0.021 0.001 ARG p 18 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 434) hydrogen bonds : angle 5.48595 ( 1245) covalent geometry : bond 0.00390 (18756) covalent geometry : angle 0.98285 (25506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 556 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8744 (t) cc_final: 0.8218 (p) REVERT: b 98 ASP cc_start: 0.8427 (m-30) cc_final: 0.8154 (m-30) REVERT: c 40 ASP cc_start: 0.7290 (m-30) cc_final: 0.6799 (m-30) REVERT: c 93 ILE cc_start: 0.8034 (pp) cc_final: 0.6645 (mt) REVERT: d 115 ASP cc_start: 0.7434 (t70) cc_final: 0.6671 (t0) REVERT: f 30 LYS cc_start: 0.8712 (ptmt) cc_final: 0.8446 (tttt) REVERT: g 111 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7504 (tm-30) REVERT: g 115 ASP cc_start: 0.7499 (t70) cc_final: 0.6692 (t0) REVERT: g 141 ASN cc_start: 0.7025 (t0) cc_final: 0.5569 (p0) REVERT: h 14 ASP cc_start: 0.6884 (m-30) cc_final: 0.6667 (m-30) REVERT: i 116 LEU cc_start: 0.8369 (pt) cc_final: 0.8071 (pt) REVERT: j 107 MET cc_start: 0.8703 (tpt) cc_final: 0.8414 (tpp) REVERT: j 115 ASP cc_start: 0.6994 (t70) cc_final: 0.6449 (t70) REVERT: k 20 PHE cc_start: 0.7608 (m-80) cc_final: 0.7234 (m-80) REVERT: n 9 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5655 (pp) REVERT: n 72 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7003 (p) REVERT: o 8 VAL cc_start: 0.7013 (t) cc_final: 0.6655 (p) REVERT: o 98 ASP cc_start: 0.6436 (t0) cc_final: 0.6209 (t0) REVERT: o 103 GLN cc_start: 0.7940 (mp10) cc_final: 0.7716 (mp10) REVERT: p 93 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8866 (pt) REVERT: q 40 ASP cc_start: 0.7421 (p0) cc_final: 0.6997 (p0) REVERT: q 105 GLN cc_start: 0.8400 (tt0) cc_final: 0.8157 (tt0) REVERT: q 130 ASP cc_start: 0.4612 (t0) cc_final: 0.4335 (t0) REVERT: r 40 ASP cc_start: 0.7702 (m-30) cc_final: 0.7115 (p0) REVERT: r 116 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6317 (pt) outliers start: 90 outliers final: 34 residues processed: 610 average time/residue: 0.3072 time to fit residues: 279.5192 Evaluate side-chains 441 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 403 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 68 ASP Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 68 ASP Chi-restraints excluded: chain h residue 55 ARG Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 83 ASP Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 115 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0904 > 50: distance: 8 - 13: 34.537 distance: 14 - 15: 69.052 distance: 14 - 17: 23.478 distance: 15 - 16: 34.568 distance: 15 - 20: 41.317 distance: 17 - 18: 18.793 distance: 17 - 19: 21.603 distance: 20 - 153: 32.386 distance: 21 - 22: 39.497 distance: 21 - 24: 40.164 distance: 22 - 23: 39.327 distance: 23 - 150: 37.181 distance: 24 - 25: 35.149 distance: 24 - 26: 41.012 distance: 27 - 28: 40.464 distance: 27 - 76: 42.680 distance: 29 - 30: 4.284 distance: 30 - 73: 46.654 distance: 32 - 33: 40.963 distance: 32 - 34: 39.074 distance: 36 - 39: 39.349 distance: 39 - 41: 60.135 distance: 43 - 44: 30.019 distance: 44 - 45: 31.035 distance: 45 - 46: 57.039 distance: 45 - 47: 40.324 distance: 47 - 48: 14.835 distance: 48 - 51: 14.583 distance: 49 - 50: 13.337 distance: 49 - 54: 28.122 distance: 51 - 53: 40.028 distance: 54 - 55: 34.526 distance: 55 - 56: 7.193 distance: 55 - 58: 33.419 distance: 58 - 59: 4.197 distance: 59 - 60: 39.880 distance: 63 - 64: 39.883 distance: 64 - 73: 49.021 distance: 67 - 68: 40.223 distance: 68 - 69: 34.177 distance: 69 - 70: 8.747 distance: 70 - 71: 32.382 distance: 70 - 72: 11.698 distance: 73 - 74: 15.973 distance: 74 - 75: 19.746 distance: 74 - 77: 3.533 distance: 75 - 76: 15.669 distance: 75 - 82: 25.292 distance: 77 - 78: 16.107 distance: 78 - 79: 6.603 distance: 79 - 80: 34.826 distance: 80 - 81: 6.479 distance: 83 - 84: 39.868 distance: 83 - 86: 38.605 distance: 84 - 85: 41.012 distance: 84 - 89: 34.126 distance: 86 - 87: 40.849